MCMCglmm-Functions_VIF_&_Kappa_by_Austin_Frank_2011_R-Hacks.R

vif.MCMCglmm <- function (fit, intercept.columns = c(1)) {
  nF <- fit$Fixed$nfl
  v <- cov(as.matrix(fit$X[,1:nF]))
  nam <- colnames(fit$Sol[,1:nF])
  
  v <- v[-intercept.columns, -intercept.columns, drop = FALSE]
  nam <- nam[-intercept.columns]
  
  d <- diag(v)^0.5
  v <- diag(solve(v/(d %o% d)))
  names(v) <- nam
  v
}

kappa.MCMCglmm <- function (fit, add.intercept = TRUE, scale = TRUE, intercept.columns = c(1)) {
  nF <- fit$Fixed$nfl
  X <- fit$X[,1:nF]
  if (with.intercept & scale) {
    kappa(cBind(rep(1), scale(X[, -intercept.columns])))
  } else if (with.intercept & !scale) {
    kappa(X)
  } else if (!add.intercept & scale) {
    kappa(scale(X[,-intercept.columns]))
  } else {
    kappa(X[,-intercept.columns])
  }
}